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Utility of the biofire filmarray pneumonia panel plus assay for syndromic testing of lower-respiratory tract infections in a low-middle-income setting
Background: Determining lower respiratory tract infection (LRTI) aetiology is complex. Culture-based methods are laborious with poor sensitivity. Molecular assays improve detection of potential pathogens, but incorrect interpretation of results may lead to inappropriate antimicrobial therapy. Method...
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| Format: | Thesis |
| Language: | English English |
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Department of Pathology
2025
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| _version_ | 1867613344079282176 |
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| access_status_str | Open Access |
| author | Van Der Westhuyzen, Mene |
| author2 | Moodley, Clinton |
| author_browse | Moodley, Clinton Van Der Westhuyzen, Mene |
| author_facet | Moodley, Clinton Van Der Westhuyzen, Mene |
| author_sort | Van Der Westhuyzen, Mene |
| collection | Thesis |
| description | Background: Determining lower respiratory tract infection (LRTI) aetiology is complex. Culture-based methods are laborious with poor sensitivity. Molecular assays improve detection of potential pathogens, but incorrect interpretation of results may lead to inappropriate antimicrobial therapy. Methods: The utility of the BioFire® FilmArray® Pneumonia Panel plus (FA-PP) to detect LRTI pathogens, and the potential antimicrobial stewardship impacts in a low resource setting, was assessed. Routine LRT samples were included from adult patients with clinically suspected LRTI or with a concomitant blood culture at Groote Schuur Hospital and referring facilities. Culture and FA-PP results were compared, and pharmacy data analysed to determine appropriateness of antibiotic therapy. Results: There was an 80% correlation between cultured LRTI pathogens and the FA-PP bin ≥107 results. Compared to culture the FA-PP detected substantially more pathogens (86,6% versus 17,9%) and produced a combined 100% positive percent agreement, and 88% negative percent agreement. The FA-PP detected bacterial-viral coinfections in 27% of samples. Correlation of FA-PP results with pharmacy data (n=69) indicated a potential antibiotic change in 75% of cases, but this is difficult to accurately characterise without a ‘gold-standard' for treatment or complete clinical data. Conclusion: The FA-PP increased the number of positive samples with typical bacteria, but the semi-quantitative reporting algorithm does not describe the correlation between the different bin values and colonization versus infection. This complicates result interpretation and may lead to inappropriate antimicrobial treatment. This study highlights the potential positive impact of rapid molecular assays for routine care in lower income settings, but also underscores the interpretive challenges associated with these tests. |
| format | Thesis |
| id | oai:open.uct.ac.za:11427/41980 |
| institution | University of Cape Town (South Africa) |
| language | English eng |
| last_indexed | 2026-06-10T12:34:39.078Z |
| license_str | Not specified — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UCTD — University of Cape Town Open Access Repository |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Department of Pathology |
| publisherStr | Department of Pathology |
| record_format | dspace |
| source_str | UCTD — University of Cape Town Open Access Repository |
| spelling | oai:open.uct.ac.za:11427/41980 Utility of the biofire filmarray pneumonia panel plus assay for syndromic testing of lower-respiratory tract infections in a low-middle-income setting Van Der Westhuyzen, Mene Moodley, Clinton Syndromic testing Background: Determining lower respiratory tract infection (LRTI) aetiology is complex. Culture-based methods are laborious with poor sensitivity. Molecular assays improve detection of potential pathogens, but incorrect interpretation of results may lead to inappropriate antimicrobial therapy. Methods: The utility of the BioFire® FilmArray® Pneumonia Panel plus (FA-PP) to detect LRTI pathogens, and the potential antimicrobial stewardship impacts in a low resource setting, was assessed. Routine LRT samples were included from adult patients with clinically suspected LRTI or with a concomitant blood culture at Groote Schuur Hospital and referring facilities. Culture and FA-PP results were compared, and pharmacy data analysed to determine appropriateness of antibiotic therapy. Results: There was an 80% correlation between cultured LRTI pathogens and the FA-PP bin ≥107 results. Compared to culture the FA-PP detected substantially more pathogens (86,6% versus 17,9%) and produced a combined 100% positive percent agreement, and 88% negative percent agreement. The FA-PP detected bacterial-viral coinfections in 27% of samples. Correlation of FA-PP results with pharmacy data (n=69) indicated a potential antibiotic change in 75% of cases, but this is difficult to accurately characterise without a ‘gold-standard' for treatment or complete clinical data. Conclusion: The FA-PP increased the number of positive samples with typical bacteria, but the semi-quantitative reporting algorithm does not describe the correlation between the different bin values and colonization versus infection. This complicates result interpretation and may lead to inappropriate antimicrobial treatment. This study highlights the potential positive impact of rapid molecular assays for routine care in lower income settings, but also underscores the interpretive challenges associated with these tests. 2025-10-02T12:04:05Z 2025-10-02T12:04:05Z 2025 2025-10-02T11:06:13Z Thesis / Dissertation Masters MMed http://hdl.handle.net/11427/41980 en eng application/pdf Department of Pathology Faculty of Health Sciences University of Cape Town |
| spellingShingle | Syndromic testing Van Der Westhuyzen, Mene Utility of the biofire filmarray pneumonia panel plus assay for syndromic testing of lower-respiratory tract infections in a low-middle-income setting |
| thesis_degree_str | Master's |
| title | Utility of the biofire filmarray pneumonia panel plus assay for syndromic testing of lower-respiratory tract infections in a low-middle-income setting |
| title_full | Utility of the biofire filmarray pneumonia panel plus assay for syndromic testing of lower-respiratory tract infections in a low-middle-income setting |
| title_fullStr | Utility of the biofire filmarray pneumonia panel plus assay for syndromic testing of lower-respiratory tract infections in a low-middle-income setting |
| title_full_unstemmed | Utility of the biofire filmarray pneumonia panel plus assay for syndromic testing of lower-respiratory tract infections in a low-middle-income setting |
| title_short | Utility of the biofire filmarray pneumonia panel plus assay for syndromic testing of lower-respiratory tract infections in a low-middle-income setting |
| title_sort | utility of the biofire filmarray pneumonia panel plus assay for syndromic testing of lower respiratory tract infections in a low middle income setting |
| topic | Syndromic testing |
| url | http://hdl.handle.net/11427/41980 |
| work_keys_str_mv | AT vanderwesthuyzenmene utilityofthebiofirefilmarraypneumoniapanelplusassayforsyndromictestingoflowerrespiratorytractinfectionsinalowmiddleincomesetting |